The Message in the Microcosm: DNA and the Death of Materialism

Stephen C. Meyer

Traditional approaches that fail to take account of new findings in molecular
cell biology cannot survive the present day. Materialistic explanations for
the origin of information have been systematically eliminated over the past
forty years. Has origin-of-life research brought us to the brink of a new scientific
revolution?

Despite the now well-documented influence of Christian thinking
on the rise of modern science from the time of Ockham to Newton,
much of science during the 19th century took a decidedly materialistic
turn. From cosmology to geology to biology, science seemed to
support the rise of materialistic thought. In field after field,
new scientific theories implied the complete autonomy of nature
from God. Materialism denied evidence of any intelligent design
in nature and any ultimate purpose to human existence.

Darwin's evolutionary theory, in particular, seemed to show
that the blind process of natural selection acting on random variations
could, and did, account for the origin of new forms of life from
simpler forms without any divine intervention or guidance. According
to Darwin, living organisms only appeared to be designed by an
intelligent creator; nature itself was the real creator of new
species. By the late 19th century only the origin of the first
life-something Darwin's theory did not address-lacked a detailed
materialistic explanation.

Explaining Life's Origin in Materialistic Terms

Nevertheless, in the 1870s and 1880s scientists assumed that
devising an explanation for the origin of life would be fairly
easy. For one thing, they assumed that life was essentially a
rather simple substance called protoplasm that could be easily
constructed by combining and recombining simple chemicals such
as carbon dioxide, oxygen, and nitrogen. Thus, the German evolutionary
biologist Ernst Haeckel would refer to cells as simple "homogeneous
globules of plasm."

To Haeckel, a living cell seemed no more complex than a blob
of jello. His theory of how life first came into existence reflected
this view. His method likened cell "autogeny," as he
called it, to the process of inorganic crystallization. Haeckel's
English counterpart, T.H. Huxley, proposed a simple two-step method
of chemical recombination to explain the origin of the first cell.
Just as salt could be produced spontaneously by adding sodium
to chloride, so thought Haeckel and Huxley, could a living cell
be produced by adding several chemical constituents together and
then allowing spontaneous chemical reactions to produce the simple
protoplasmic substance that they assumed to be the essence of
life.

During the 1920s and 1930s a more sophisticated version of
this so-called "chemical evolutionary theory" was proposed
by a Russian biochemist named Alexander I. Oparin. Oparin had
a much more accurate understanding of the complexity of cellular
metabolism, but neither he, nor any one else in the 1930s, fully
appreciated the complexity of the molecules such as protein and
DNA that make life possible. Oparin, like his 19th-century predecessors,
suggested that life could have first evolved as the result of
a series of chemical reactions. Unlike his predecessors, however,
he envisioned that this process of chemical evolution would involve
many more chemical transformations and reactions and many hundreds
of millions (or even billions) of years.

The first experimental support for Oparin's hypothesis came
in December of 1952. While doing graduate work under Harold Urey
at the University of Chicago, Stanley Miller conducted the first
experimental test of the Oparin chemical evolutionary model. Miller
circulated a gaseous mixture of methane, ammonia, water vapor,
and hydrogen through a glass vessel containing an electrical discharge
chamber. Miller sent a high voltage charge of electricity into
the chamber via tungsten filaments in an attempt to simulate the
effects of ultraviolet light on prebiotic atmospheric gases. After
two days, Miller found a small (2%) yield of amino acids in the
U-shaped water trap he used to collect reaction products at the
bottom of the vessel.

Miller's success in producing biologically relevant "building
blocks" under ostensibly prebiotic conditions was heralded
as a great breakthrough. His experiment seemed to provide experimental
support for Oparin's chemical evolutionary theory by showing that
an important step in Oparin's scenario-the production of biological
building blocks from simpler atmospheric gases-was possible on
the early earth.

Miller's experimental results also received widespread press
coverage in popular publications such as Time magazine
and gave Oparin's model the status of textbook orthodoxy almost
overnight. Thanks largely to Miller's experimental work, chemical
evolution is now routinely presented in both high school and college
biology textbooks as the accepted scientific explanation for the
origin of life.

Yet as we shall see, chemical evolutionary theory is now known
to be riddled with difficulties; and Miller's work is understood
by the origin-of-life research community itself to have little
if any relevance to explaining how amino acids-let alone proteins
or living cells-actually could have arisen on the early earth.

To understand today's growing crisis in chemical evolutionary
theory, this article will focus on the two most severe difficulties
confronting it: the problem of hostile pre-biotic conditions and
the problem posed by the complexity of the cell and its components.

The Problem of Hostile Pre-biotic Conditions

When Stanley Miller conducted his experiment simulating the
production of amino acids on the early earth, he presupposed that
the earth's atmosphere was composed of a mixture of what chemists
call reducing gases such as methane, ammonia, and hydrogen. He
also assumed that the earth's atmosphere contained virtually no
free oxygen. In the years following Miller's experiment, however,
new geochemical evidence made it clear that the assumptions that
Oparin and Miller had made about the early atmosphere could not
be justified.

Instead, evidence strongly suggested that neutral gases-not
methane, ammonia, and hydrogen-predominated in the early atmosphere.
Moreover, a number of geochemical studies showed that significant
amounts of free oxygen were also present even before the advent
of plant life, probably as the result of volcanic outgassing and
the photodissociation of water vapor.

In a chemically neutral atmosphere, reactions among atmospheric
gases will not take place readily. Moreover, even a small amount
of atmospheric oxygen will quench the production of biological
building blocks and cause any biomolecules otherwise present to
degrade rapidly.

As had been well known even before Miller's experiment, amino
acids will form readily in an appropriate mixture of reducing
gases. What made Miller's experiment significant was not the production
of amino acids per se, but the production of amino acids
from presumably plausible prebiotic conditions. As Miller himself
stated, "In this apparatus an attempt was made to duplicate
a primitive atmosphere of the earth, and not to obtain the optimum
conditions for the formation of amino acids." Now, however,
the situation has changed. The only reason to continue assuming
the existence of a chemically-reducing, prebiotic atmosphere is
that chemical evolutionary theory requires it.

Ironically, even if we assume for the moment that the reducing
gases used by Stanley Miller do actually simulate conditions on
the early Earth, his experiments inadvertently demonstrated the
necessity of intelligent agency. Even successful simulation experiments
require the intervention of the experimenters to prevent what
are known as "interfering cross reactions" and other
chemically destructive processes. Without human intervention,
Miller-type experiments invariably produce non-biological substances
that degrade amino acids into non-biologically relevant compounds.

Experimenters prevent this by removing chemical products that
induce undesirable cross reactions. They employ other "unnatural"
interventions as well. Simulation experimenters have typically
used only short wavelength light, rather than both short and long
wavelength ultraviolet light, which would be present in any realistic
atmosphere. Why? The presence of the long wavelength UV light
quickly degrades amino acids.

Such manipulations constitute what chemist Michael Polanyi
called a "profoundly informative intervention." They
seem to "simulate," if anything, the need for an intelligent
agent to overcome the randomizing influences of natural chemical
processes.

The Problem of Specific Sequencing

Yet a more fundamental problem remains for all chemical evolutionary
scenarios. Even if it could be demonstrated that the building
blocks of essential molecules could arise in realistic prebiotic
conditions, the problem of assembling those building blocks into
functioning proteins or DNA chains would remain. This problem
of explaining the specific sequencing and thus, the information
within biopolymers, lies at the heart of the current crisis in
materialistic evolutionary thinking.

During the 1950s and 60s, at roughly the same time molecular
biologists found that protein molecules were composed of long
and definitely arranged sequences of amino acids, scientists also
learned the structure and function of DNA, the molecule of heredity.
Molecular biologists discovered that the specificity of amino
acids in proteins derives from a prior specificity within the
DNA molecule-from information on the DNA molecule stored as millions
of specifically arranged chemicals called nucleotides or bases
along the spine of DNA's helical strands. So the sequence specificity
of proteins depends upon another sequence specificity-upon information-encoded
in DNA.

The elucidation of this system by molecular biologists has
raised the question of the ultimate origin of the specificity-the
information-in both DNA and proteins. Indeed, many scientists
now refer to the information problem as the "Holy Grail"
of origin-of-life biology. As Bernd-Olaf Kuppers recently stated,
"the problem of the origin of life is clearly basically equivalent
to the problem of the origin of biological information."

Explaining the Origin of Information

While many outside origin-of-life biology may still invoke
"chance" as a causal explanation for the origin of biological
information, few serious researchers still do. Since molecular
biologists began to appreciate the sequence specificity of proteins
and nucleic acids in the 1950s and 60s, many calculations have
been made to determine the probability of formulating functional
proteins and nucleic acids at random. Even assuming extremely
favorable prebiotic conditions (whether realistic or not) and
theoretically maximal reaction rates, such calculations have invariably
shown that the probability of obtaining functionally sequenced
biomacromolecules at random is, in Prigogine's words, "vanishingly
small ... even on the scale of ... billions of years." As
Cairns-Smith wrote:

Blind chance ... is very limited. Low-levels of cooperation
he [blind chance] can produce exceedingly easily (the equivalent
of letters and small words), but he becomes very quickly incompetent
as the amount of organization increases. Very soon indeed long
waiting periods and massive material resources become irrelevant.

Consider the probabilistic hurdles that must be overcome to
construct even one short protein molecule of about one hundred
amino acids in length. First, all amino acids must form a chemical
bond known as a peptide bond so as to join with other amino acids
in the protein chain. Yet in nature many other types of chemical
bonds are possible between amino acids. The probability of building
a chain of 100 amino acids in which all linkages involve peptide
bonds is roughly 1 chance in 1030. Second,
functioning proteins tolerate only left-handed amino acids.

Third and most important of all: functioning proteins must
have amino acids that link up in a specific sequential arrangement,
just as the letters in a meaningful sentence. Because there are
twenty biologically occurring amino acids the probability of getting
a specific amino acid at a given site is 1/20. Actually the probability
is even lower because there are many non-proteinous amino acids
in nature. Even if we assume that some sites along the chain will
tolerate several amino acids (using the variances determined by
biochemist Robert Sauer of M.I.T.), we find that the probability
of achieving a functional sequence of amino acids in several functioning
proteins at random is still "vanishingly small," roughly
1 chance in 1065-an astronomically large
number.

Moreover, if one also factors in the probability of attaining
proper bonding and optical isomers, the probability of constructing
a rather short, functional protein at random becomes so small
as to be effectively zero (1 chance in 10125)
even given our multi-billion-year-old universe. Such calculations,
thus, simply reinforce the opinion that has prevailed since the
mid-1960s within origin-of-life biology: chance is not an adequate
explanation for the origin of biological complexity and specificity.

Natural Selection as an Explanation

At nearly the same time that many researchers became disenchanted
with "chance" explanations, theories of pre-biotic natural
selection also fell out of favor. Such theories allegedly overcome
the difficulties of pure chance by providing a mechanism by which
complexity-increasing events in the cell might be preserved and
selected. Yet these theories share many of the difficulties that
afflict purely chance-based theories.

Oparin's revised theory, for example, seemed to presuppose
a pre-existing mechanism of self-replication. Self-replication
in all extant cells depends upon functional (and, therefore, to
a high degree sequence-specific) proteins and nucleic acids. Yet
the origin of these molecules is precisely what Oparin needed
to explain. Thus, many rejected the postulation of pre-biotic
natural selection as question begging.

Further, natural selection can only select what chance has
first produced, and chance, at least in a prebiotic setting, seems
an implausible agent for producing the information present in
even a single functioning protein or DNA molecule. For this reason,
most scientists now dismiss appeals to prebiotic natural selection
as essentially indistinguishable from appeals to chance.

Self-Organization as an Explanation

Because of these difficulties, many origin-of-life theorists
after the mid-1960s attempted to address the problem of the origin
of biological information in a completely new way. Rather than
invoking prebiotic natural selection or "frozen accidents,"
many theorists suggested that the laws of nature and chemical
attraction may themselves be responsible for the information in
DNA and proteins. Some have suggested that simple chemicals might
possess "self-ordering properties" capable of organizing
the constituent parts of proteins, DNA and RNA into the specific
arrangements they now possess.

In 1977, Prigogine and Nicolis proposed a theory of self-organization
based on their observation that open systems driven far from equilibrium
often display self-ordering tendencies. For example, gravitational
energy will produce highly ordered vortices in a draining bathtub;
and thermal energy flowing through a heat sink will generate distinctive
convection currents or "spiral wave activity."

For many current origin-of-life scientists, self-organizational
models now seem to offer the most promising approach to explaining
the origin of biological information. Nevertheless, critics have
called into question both the plausibility and the relevance of
self-organizational models. Ironically, perhaps the most prominent
early advocate of self-organization, Professor Dean Kenyon, has
now explicitly repudiated such theories as both incompatible with
empirical findings and theoretically incoherent.

The empirical difficulties attendant self-organizational scenarios
can be illustrated by examining a DNA molecule. The diagram here
shows that the structure of DNA depends upon several chemical
bonds. There are bonds, for example, between the sugar and the
phosphate molecules that form the two twisting backbones of the
DNA molecule. There are bonds fixing individual (nucleotide) bases
to the sugar-phosphate backbones on each side of the molecule.
Yet notice that there are no chemical bonds between the bases
that run along the spine of the helix. Yet it is precisely along
this axis of the molecule that the genetic instructions in DNA
are encoded.

Further, just as magnetic letters can be combined and recombined
in any way to form various sequences on a metal surface, so too
can each of the four bases A, T, G, and C attach to any site on
the DNA backbone with equal facility, making all sequences equally
probably (or improbable). The same type of chemical bond occurs
between the bases and the backbone regardless of which base attaches.
All four bases are acceptable; none is preferred. In other words,
differential bonding affinities do not account for the
sequencing of the bases. Because these same facts hold for RNA
molecules, researchers who speculate that life began in an "RNA
world" have also failed to solve the sequencing problem-i.e.,
the problem of explaining how information present in all functioning
RNA molecules could have arisen in the first place.

For those who want to explain the origin of life as the result
of self-organizing properties intrinsic to the material constituents
of living systems, these rather elementary facts of molecular
biology have devastating implications. The most logical place
to look for self-organizing properties to explain the origin of
genetic information is in the constituent parts of the molecules
carrying that information. But biochemistry and molecular biology
make clear that the forces of attraction between the constituents
in DNA, RNA, and protein do not explain the sequence specificity
of these large information-bearing biomolecules.

Significantly, information theorists insist that there is a
good reason for this. If chemical affinities between the constituents
in the DNA message text determined the arrangement of the text,
such affinities would dramatically diminish the capacity of DNA
to carry information. To illustrate, consider what would happen
if the individual nucleotide "letters" (A,T,G,C) in
a DNA molecule did interact by chemical necessity
with each other. Every time adenine (A) occurred in a growing
genetic sequence, it would likely drag thymine (T) along with
it. Every time cytosine (C) found a slot, guanine (G) would follow.
As a result, the DNA message text would be peppered with repeating
sequences of A's followed by T's and C's followed by G's.

Rather than having a genetic molecule capable of unlimited
novelty, with all the unpredictable and aperiodic sequences that
characterize informative texts, we would have a highly repetitive
text awash in redundant sequences-much as happens in crystals.
Indeed, in a crystal the forces of mutual chemical attraction
do completely explain the sequential ordering of the constituent
parts, and consequently crystals cannot convey novel information.
Sequencing in crystals is repetitive and highly ordered, but not
informative. Once one has seen "Na" followed by "Cl"
in a crystal of salt, for example, one has seen the extent of
the sequencing possible.

Bonding affinities, to the extent they exist, mitigate against
the maximization of information. They cannot, therefore, be used
to explain the origin of information. Affinities create mantras,
not messages.

The tendency to confuse the qualitative distinction between
"order" and "information" has characterized
self-organizational research efforts and calls into question the
relevance of such work to the origin of life. Self-organizational
theorists explain well what doesn't need explaining. What needs
explaining is not the origin of order (whether in the form of
crystals, swirling tornadoes or the "eyes" of hurricanes),
but the origin of information-the highly improbable, aperiodic,
and yet specified sequences that make biological function possible.

For Help, Call Information

To see the distinction between order and information compare
the sequence "ABABABABABABAB" to the sequence "Help!
Our neighbor's house is on fire!" The first sequence is repetitive
and ordered, but not complex or informative. Systems that are
characterized by both specificity and complexity (what information
theorists call "specified complexity") have "information
content." Since such systems have the qualitative feature
of aperiodicity or complexity, they are qualitatively distinguishable
from systems characterized by simple periodic order. Thus, attempts
to explain the origin of order have no relevance to discussions
of the origin of information content. Significantly, the nucleotide
sequences in the coding regions of DNA have, by all accounts,
a high information content-that is, they are both highly specified
and complex, just like meaningful English sentences.

Yet the information contained in an English sentence-in a newspaper,
for example-does not derive from the chemistry of the ink or paper,
but from a source extrinsic to physics and chemistry altogether.
Indeed the message transcends the properties of the medium.

The information in DNA also transcends the properties of its
material medium. Because chemical bonds do not determine the arrangement
of nucleotide bases, the nucleotides can assume a vast array of
possible sequences and thereby express many different messages.

If the properties of matter (i.e., the medium) do not suffice
to explain the origin of information, what does? Our experience
with information-intensive systems (especially codes and languages)
indicates that such systems always come from an intelligent source-i.e.,
from mental or personal agents, not chance or material necessity.

Our generalization about the cause of information has, ironically,
also received confirmation from origin-of-life research itself.
During the last forty years, every naturalistic model proposed
has failed to explain the origin of information-the great stumbling
block for materialistic scenarios. Thus, mind or intelligence
or what philosophers call "agent causation," now stands
as the only cause known to be capable of creating an information-rich
system, including the coding regions of DNA, functional proteins,
and the cell as a whole.

The Design Inference

Because mind or intelligent design is a necessary cause of
an informative system, one can detect the past action of an intelligent
cause from the presence of an information-intensive effect, even
if the cause itself cannot be directly observed. Since information
requires an intelligent source, the flowers spelling "Welcome
to Victoria" in the gardens of Victoria harbor lead visitors
to infer the activity of intelligent agents even if they did not
see the flowers planted and arranged.

Scientists in many fields now recognize the connection between
intelligence and information and make inferences accordingly.
Archaeologists assume a mind produced the inscriptions on the
Rosetta Stone. SETI's search for extraterrestrial intelligence
presupposes that the presence of information imbedded in electromagnetic
signals from space would indicate an intelligent source. As yet,
radio astronomers have not found information-bearing signals coming
from space. But molecular biologists, looking closer to home,
have identified encoded information in the cell. Consequently,
a growing number of scientists now suggest that the information
in DNA justifies making what probability theorist William Dembski
and biochemist Michael Behe call "the design inference."

The materialistic science we have inherited from the late 19th
century, with its exclusive conceptual reliance on matter and
energy, could neither envision nor can it now account for today's
biology. As Norbert Weiner puts it, "Information is information,
neither energy nor matter. No materialism that fails to take account
of this can survive the present day."

The molecular biology of the cell raises the possibility that
"no materialism" will survive the revolution beginning
to take root in science. While established journals and institutions
continue to propagate the orthodoxies of a generation ago, many
scientists, philosophers of science, and mathematicians have begun
to challenge these views and to formulate alternative approaches.

If the simplest life owes its origin to an intelligent Creator,
then perhaps man is not the "cosmic orphan" that 20th-century
scientific materialism has suggested. Perhaps then, during the
21st century, the traditional moral and spiritual foundations
of the West will find support from the very sciences that once
seemed to undermine them.